T1DBase - A Bioinformatics Resource for Type 1 Diabetes Researchers

General Information: Available

Organism	Human
Points of Interest	rs6920220; rs10499194
Karyotype Band Location	6q23.3
Chromosomal Location (GRCh37)	Chr6:137873690-138338256
Region Size	0.46 Mb
Orthologous Regions	Mouse: Human 6q23.3 Orthologous Region Rat: Human 6q23.3 Orthologous Region
Genes in Region (4)	LOC100130476, LOC100507406, LOC100507429, TNFAIP3

View this region in the Human T1D Regions table.

Marker	Marker Source	Start	Strand	Peptide Shift	Gene Symbol (HGNC)	Gene ID (Entrez)	Amino Acid Position
rs149162594	dbSNP_134	138192426	+	I/T	TNFAIP3	7128	21
rs148028402	dbSNP_134	138192601	+	S/R	TNFAIP3	7128	79
rs112229105	dbSNP_134	138192612	+	L/P	TNFAIP3	7128	83
rs146534657	dbSNP_134	138195991	+	N/S	TNFAIP3	7128	102
rs141856349	dbSNP_134	138196008	+	T/A	TNFAIP3	7128	108
rs150717698	dbSNP_134	138196029	+	V/I	TNFAIP3	7128	115
rs5029941	dbSNP_134	138196060	+	A/V	TNFAIP3	7128	125
rs2230926	dbSNP_134	138196066	+	F/C	TNFAIP3	7128	127
rs144788826	dbSNP_134	138196171	+	R/Q	TNFAIP3	7128	162
rs147932545	dbSNP_134	138196889	+	S/N	TNFAIP3	7128	184
rs34935799	dbSNP_134	138196896	+	L/L	TNFAIP3	7128	186
rs141807543	dbSNP_134	138196957	+	I/L	TNFAIP3	7128	207
rs145706326	dbSNP_134	138197139	+	M/R	TNFAIP3	7128	214
rs151032703	dbSNP_134	138197175	+	P/H	TNFAIP3	7128	226
rs61756235	dbSNP_134	138197259	+	S/N	TNFAIP3	7128	254
rs140951984	dbSNP_134	138197270	+	V/I	TNFAIP3	7128	258
rs150198888	dbSNP_134	138198245	+	R/W	TNFAIP3	7128	280
rs145745293	dbSNP_134	138198326	+	L/V	TNFAIP3	7128	307
rs140616865	dbSNP_134	138199775	+	V/A	TNFAIP3	7128	398
rs144728856	dbSNP_134	138199883	+	A/V	TNFAIP3	7128	434
rs143619694	dbSNP_134	138199926	+	W/C	TNFAIP3	7128	448
rs141614391	dbSNP_134	138200083	+	A/T	TNFAIP3	7128	501
rs150513567	dbSNP_134	138200087	+	R/Q	TNFAIP3	7128	502
rs140357085	dbSNP_134	138200131	+	D/N	TNFAIP3	7128	517
rs142752989	dbSNP_134	138200216	+	A/V	TNFAIP3	7128	545
rs150056192	dbSNP_134	138200342	+	P/L	TNFAIP3	7128	587
rs145392420	dbSNP_134	138200353	+	L/M	TNFAIP3	7128	591
rs142253225	dbSNP_134	138201240	+	T/P	TNFAIP3	7128	647
rs140610274	dbSNP_134	138201337	+	I/T	TNFAIP3	7128	679
rs3734553	dbSNP_134	138202200	-	R/Q	TNFAIP3	7128	706
rs146720688	dbSNP_134	138202250	+	N/D	TNFAIP3	7128	723
rs150355046	dbSNP_134	138202314	+	G/D	TNFAIP3	7128	744
rs138068339	dbSNP_134	138202337	+	P/S	TNFAIP3	7128	752
rs5029957	dbSNP_134	138202379	+	A/P	TNFAIP3	7128	766
rs143002189	dbSNP_134	138202447	+	M/I	TNFAIP3	7128	788

Non-Synonymous SNPs in region dbSNP134:

(Human) GRCh37 - chr6:137873690..138338256 (464.57 kb) View in Genome Browser

An overview of the region is provided by GBrowse. Tracks shown include gene information and study-specific data:
Immune Disease Associated Variants	Variants shown to be associated with different auto-immune diseases
P-values, -log(p)	1 degree of freedom p-values, stratified by geographic location. Generated using snpMatrix with data from the T1DGC Meta-analysis study.
HapMap Recobination Data	Genome-wide recombination rate from Phase 2 HapMap estimated from phased haplotypes in HapMap Release 22 (NCBI 36). Units are in cM/Mb, coordinates have been projected to the current build.

Genes in LD Region: Available

Summary data derived from GWA meta analysis Barrett et al. LD regions were calculated using different r² and D' threshold values, and these regions were then examined for genes. The definition of a gene location includes a 3kb flanking region either side of the gene.

Marker Data

Region Data

Links

r² Threshold

D' Threshold

Region

Genes

Marker	rs6920220
Chr	6
Position	138006504
Strand
P-Value	7.99e-04

N/A

0.5

chr6: 137939449..138109344

LOC100507406

LD Region Feature File

LD File

0.4

N/A

chr6: 137959235..138006504

0.8

N/A

chr6: 137959235..138006504

1

N/A

chr6: 138003822..138006504

Marker	rs10499194
Chr	6
Position	138002637
Strand
P-Value	0.000

N/A

0.5

chr6: 137957889..138082845

LOC100507406

LD Region Feature File

LD File

0.4

N/A

chr6: 137959118..138023242

0.8

N/A

chr6: 137961013..138011151

1

N/A

chr6: 138002637..138011151

Publications: 9

Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47.
Anderson CA, Boucher G, Lees CW, Franke A, D'Amato M, Taylor KD, Lee JC, Goyette P, Imielinski M, Latiano A, Lagacé C, Scott R, Amininejad L, Bumpstead S, Baidoo L, Baldassano RN, Barclay M, Bayless TM, Brand S, Büning C, Colombel JF, Denson LA, De Vos M, Dubinsky M, Edwards C, Ellinghaus D, Fehrmann RS, Floyd JA, Florin T, Franchimont D, Franke L, Georges M, Glas J, Glazer NL, Guthery SL, Haritunians T, Hayward NK, Hugot JP, Jobin G, Laukens D, Lawrance I, Lémann M, Levine A, Libioulle C, Louis E, McGovern DP, Milla M, Montgomery GW, Morley KI, Mowat C, Ng A, Newman W, Ophoff RA, Papi L, Palmieri O, Peyrin-Biroulet L, Panés J, Phillips A, Prescott NJ, Proctor DD, Roberts R, Russell R, Rutgeerts P, Sanderson J, Sans M, Schumm P, Seibold F, Sharma Y, Simms LA, Seielstad M, Steinhart AH, Targan SR, van den Berg LH, Vatn M, Verspaget H, Walters T, Wijmenga C, Wilson DC, Westra HJ, Xavier RJ, Zhao ZZ, Ponsioen CY, Andersen V, Torkvist L, Gazouli M, Anagnou NP, Karlsen TH, Kupcinskas L, Sventoraityte J, Mansfield JC, Kugathasan S, Silverberg MS, Halfvarson J, Rotter JI, Mathew CG, Griffiths AM, Gearry R, Ahmad T, Brant SR, Chamaillard M, Satsangi J, Cho JH, Schreiber S, Daly MJ, Barrett JC, Parkes M, Annese V, Hakonarson H, Radford-Smith G, Duerr RH, Vermeire S, Weersma RK, Rioux JD
Nat Genet. 2011
PubMed ID: 21297633
Investigation of potential non-HLA rheumatoid arthritis susceptibility loci in a European cohort increases the evidence for nine markers.
Plant D, Flynn E, Mbarek H, Dieudé P, Cornelis F, Arlestig L, Dahlqvist SR, Goulielmos G, Boumpas DT, Sidiropoulos P, Johansen JS, Ørnbjerg LM, Hetland ML, Klareskog L, Filer A, Buckley CD, Raza K, Witte T, Schmidt RE, Worthington J
Ann Rheum Dis. 2010
PubMed ID: 20498205
Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci.
Stahl EA, Raychaudhuri S, Remmers EF, Xie G, Eyre S, Thomson BP, Li Y, Kurreeman FA, Zhernakova A, Hinks A, Guiducci C, Chen R, Alfredsson L, Amos CI, Ardlie KG, BIRAC Consortium, Barton A, Bowes J, Brouwer E, Burtt NP, Catanese JJ, Coblyn J, Coenen MJ, Costenbader KH, Criswell LA, Crusius JB, Cui J, de Bakker PI, De Jager PL, Ding B, Emery P, Flynn E, Harrison P, Hocking LJ, Huizinga TW, Kastner DL, Ke X, Lee AT, Liu X, Martin P, Morgan AW, Padyukov L, Posthumus MD, Radstake TR, Reid DM, Seielstad M, Seldin MF, Shadick NA, Steer S, Tak PP, Thomson W, van der Helm-van Mil AH, van der Horst-Bruinsma IE, van der Schoot CE, van Riel PL, Weinblatt ME, Wilson AG, Wolbink GJ, Wordsworth BP, YEAR Consortium, Wijmenga C, Karlson EW, Toes RE, de Vries N, Begovich AB, Worthington J, Siminovitch KA, Gregersen PK, Klareskog L, Plenge RM
Nat Genet. 2010
PubMed ID: 20453842
Multiple common variants for celiac disease influencing immune gene expression.
Dubois PC, Trynka G, Franke L, Hunt KA, Romanos J, Curtotti A, Zhernakova A, Heap GA, Adány R, Aromaa A, Bardella MT, van den Berg LH, Bockett NA, de la Concha EG, Dema B, Fehrmann RS, Fernández-Arquero M, Fiatal S, Grandone E, Green PM, Groen HJ, Gwilliam R, Houwen RH, Hunt SE, Kaukinen K, Kelleher D, Korponay-Szabo I, Kurppa K, MacMathuna P, Mäki M, Mazzilli MC, McCann OT, Mearin ML, Mein CA, Mirza MM, Mistry V, Mora B, Morley KI, Mulder CJ, Murray JA, Núñez C, Oosterom E, Ophoff RA, Polanco I, Peltonen L, Platteel M, Rybak A, Salomaa V, Schweizer JJ, Sperandeo MP, Tack GJ, Turner G, Veldink JH, Verbeek WH, Weersma RK, Wolters VM, Urcelay E, Cukrowska B, Greco L, Neuhausen SL, McManus R, Barisani D, Deloukas P, Barrett JC, Saavalainen P, Wijmenga C, van Heel DA
Nat Genet. 2010
PubMed ID: 20190752
A large-scale replication study identifies TNIP1, PRDM1, JAZF1, UHRF1BP1 and IL10 as risk loci for systemic lupus erythematosus.
Gateva V, Sandling JK, Hom G, Taylor KE, Chung SA, Sun X, Ortmann W, Kosoy R, Ferreira RC, Nordmark G, Gunnarsson I, Svenungsson E, Padyukov L, Sturfelt G, Jönsen A, Bengtsson AA, Rantapää-Dahlqvist S, Baechler EC, Brown EE, Alarcón GS, Edberg JC, Ramsey-Goldman R, McGwin G, Reveille JD, Vilá LM, Kimberly RP, Manzi S, Petri MA, Lee A, Gregersen PK, Seldin MF, Rönnblom L, Criswell LA, Syvänen AC, Behrens TW, Graham RR
Nat Genet. 2009
PubMed ID: 19838195
Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes.
Barrett JC, Clayton DG, Concannon P, Akolkar B, Cooper JD, Erlich HA, Julier C, Morahan G, Nerup J, Nierras C, Plagnol V, Pociot F, Schuilenburg H, Smyth DJ, Stevens H, Todd JA, Walker NM, Rich SS, The Type 1 Diabetes Genetics Consortium
Nat Genet. 2009
PubMed ID: 19430480
Analysis of 17 autoimmune disease-associated variants in type 1 diabetes identifies 6q23/TNFAIP3 as a susceptibility locus.
Fung EY, Smyth DJ, Howson JM, Cooper JD, Walker NM, Stevens H, Wicker LS, Todd JA
Genes Immun. 2009
PubMed ID: 19110536
Rheumatoid arthritis susceptibility loci at chromosomes 10p15, 12q13 and 22q13.
Barton A, Thomson W, Ke X, Eyre S, Hinks A, Bowes J, Plant D, Gibbons LJ, Wellcome Trust Case Control Consortium, YEAR Consortium, BIRAC Consortium, Wilson AG, Bax DE, Morgan AW, Emery P, Steer S, Hocking L, Reid DM, Wordsworth P, Harrison P, Worthington J
Nat Genet. 2008
PubMed ID: 18794857
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.
Wellcome Trust Case Control Consortium
Nature. 2007
PubMed ID: 17554300

Signal Clouds: Available

6q23.3